[English] 日本語
Yorodumi
- PDB-1hnb: CRYSTAL STRUCTURE OF HUMAN CLASS MU GLUTATHIONE TRANSFERASE GSTM2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hnb
TitleCRYSTAL STRUCTURE OF HUMAN CLASS MU GLUTATHIONE TRANSFERASE GSTM2-2: EFFECTS OF LATTICE PACKING ON CONFORMATIONAL HETEROGENEITY
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE(GLUTATHIONE)
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / linoleic acid metabolic process / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / cellular response to caffeine ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / linoleic acid metabolic process / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / cellular response to caffeine / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / intercellular bridge / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / sarcoplasmic reticulum / fatty acid binding / transmembrane transporter binding / enzyme binding / protein homodimerization activity / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE S-(2,4 DINITROBENZENE) / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsRaghunathan, S. / Chandross, R.J. / Kretsinger, R.H. / Allison, T.J. / Penington, C.J. / Rule, G.S.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity.
Authors: Raghunathan, S. / Chandross, R.J. / Kretsinger, R.H. / Allison, T.J. / Penington, C.J. / Rule, G.S.
#1: Journal: Biochemistry / Year: 1992
Title: Mapping of the Substrate-Binding Site of a Human Class Mu Glutathione Transferase Using Nuclear Magnetic Resonance Spectroscopy
Authors: Penington, C.R. / Rule, G.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Cloning, Expression, and Characterization of a Class Mu Glutathione Transferase from Human Muscle, the Product of the Gst4 Locus
Authors: Vorachek, W.R. / Pearson, W.R. / Rule, G.S.
History
DepositionOct 15, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1604
Polymers51,2132
Non-polymers9472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-17 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.000, 86.080, 105.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 60 / 2: CIS PROLINE - PRO B 38 / 3: CIS PROLINE - PRO B 60

-
Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 25606.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P28161, glutathione transferase
#2: Chemical ChemComp-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE)


Mass: 473.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N5O10S
Nonpolymer detailsALTHOUGH CRYSTALS WERE GROWN IN THE PRESENCE OF GLUTATHIONE S-(2,4 DINITROBENZENE), ONLY THE ...ALTHOUGH CRYSTALS WERE GROWN IN THE PRESENCE OF GLUTATHIONE S-(2,4 DINITROBENZENE), ONLY THE GLUTATHIONE PORTION HAS OBSERVABLE DENSITY. COORDINATES ARE REPORTED FOR THE GLUTATHIONE PORTION ONLY (RESIDUE GDN).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.4 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1130 mg/mlenzyme1drop0.18 ml
21 MGS-DNB1drop0.0156 ml
3150 mMTris-HCl1reservoir
45 mMBME1reservoir
525-30 %PEG10001reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.5 Å / Num. obs: 6732 / % possible obs: 95 % / Redundancy: 2.9 % / Num. measured all: 19494 / Rmerge(I) obs: 0.084 / Biso Wilson estimate: 11.35 Å2
Reflection shell
*PLUS
Mean I/σ(I) obs: 7.8

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→10 Å / σ(F): 0
Details: THE ELECTRON DENSITY FOR RESIDUES 203 - 217 IS POORLY DEFINED. THE TEMPERATURE FACTORS WERE NOT REFINED TO CONVERGENCE.
RfactorNum. reflection
Rwork0.207 -
obs0.207 6408
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 40 0 3648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 6408 / Rfactor obs: 0.207 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.31

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more